German naval bases were attacked, from the second day of the war. Not by the Fleet Air Arm initially; aircraft carriers mounted anti-submarine patrols as the war started but the loss of Courageous to a U-boat on September 17th 1939 and submarine and air attacks on Ark Royal in that month demonstrated the dangers of operating around the UK. It was the RAF's Bomber Command that raided Wilhelmshaven.

Strictly speaking, it wasn't the naval base that was attacked, it was ships in the harbour; there were great concerns over potential civilian casualties, especially after President Roosevelt urged restraint, to the point that Bomber Command were forbidden from attacking targets on German soil including ships alongside a dockyard wharf. This left few potential options for Bomber Command, so its activities for the first months of the war were restricted to dropping leaflets by night, and searching for German ships in harbours or at sea by day. Bombers were dispatched on the first day of the war, September 3rd 1939, but failed to find targets; the following day 15 Blenheims and 14 Wellingtons took off to attack ships in Wilhelmshaven harbour and off Brunsbüttel at the mouth of the Kiel Canal. The results demonstrated how poorly prepared Bomber Command were; five Blenheims and two Wellingtons were shot down for negligible results. Admiral Scheer was hit by three bombs that failed to explode, the only damage done to shipping was by a Blenheim that crashed into Emden. The town of Esbjerg in Denmark was hit by two bombs intended for Brunsbüttel, 110 miles away.

Over the following months many sorties were flown searching for German shipping, seldom finding much less successfully attacking anything. On December 14th 1939 five Wellingtons were shot down near Wilhemshaven; on December 18th a further 12 Wellingtons were lost in The Battle of Heligoland Bight, after which the RAF restricted daylight operations over Germany, searching for shipping in the North Sea (with little success) and mounting harassing patrols around seaplane bases.

As the war developed Bomber Command continued intermittent attacks on naval bases joined by the US Army Air Force from 1943 (the Fleet Air Arm tended to operate further afield, such as its extremely successful attack on the Italian naval base of Taranto, though also mounted several raids on the battleship Tirpitz in Norway). Following the invasion of France ports such as Brest, Lorient, and Saint-Nazaire became important bases, as well as sites in Germany and Norway. Results varied, with bases seldom being put entirely out of action, but ships and facilities were frequently damaged (such as the battlecruiser Gneisenau, damaged several times by air attack from March 1941 to February 1942 to the point that it was ultimately decommissioned). To protect the U-boats colossal concrete bunkers were constructed, and were largely impervious to bombs until the massive Tallboy and Grand Slam bombs were deployed in 1944.

The British bombed German naval bases many times. The great majority of the attacks were by Bomber Command (i.e., by land-based bombers), but some attacks used aircraft carriers.

Britain entered WWII with shipping and naval bases as the only targets for its bombers. At the start of WWII, President Roosevelt (of the still-neutral USA) asked the combatants to restrain themselves from bombing civilian targets, and Britain, France, and Germany all agreed. British bombers could reach most of Germany from their bases in Britain, but couldn't reach eastern Germany and therefore couldn't direct support Poland in their defence against the German invasion. Unwillingness to violate the neutral airspace of Belgium and the Netherlands effectively removed some targets. Bomber Command initially treated possible collateral damage to civilian targets with great caution, and decided not to bomb any targets with too great a risk of civilian casualties. This left naval bases in western Germany and German military shipping as their targets - shipping could be attacked at sea with no civilian risk, and naval bases could be attacked with minimal chance of hitting civilian areas (provided the bombers flew appropriate bomb runs, where short or long bombs would hit the coast rather than the city). Bomber Command would fly over other targets, but dropping propaganda leaflets rather than bombs. This would continue to the end of the "Phony War", the quiet period between the defeat of Poland and the German attack in the west (the specific trigger for the change of policy was the German bombing of Rotterdam, with about 1,000 civilian deaths (fewer than the 30,000 claimed by contemporary propaganda, but still many)).

The problem with this shipping-and-bases bombing policy was that level bombers found it difficult to hit ships at sea, and German naval bases in the west, well-known to be within range of British bombers, had the best air defences available at the time (anti-aircraft guns, fighter bases, and radar). From September through to mid-December 1939, Bomber Command attempted to bomb German naval bases, especially Wilhelmshaven. These raids inflicted very little damage (Admiral Scheer was hit by three bombs, none of which exploded, and Emden was hit by a crashing Blenheim, which caused minor damage), and many suffered losses of over half of the attacking bombers. The British bomber from higher altitudes, trying get above the ceiling of German anti-aircraft fire, but losses were still heavy. Meanwhile, night raids (dropping leaflets) took very few losses, and Bomber Command switched to a policy of night bombing.

The British continued to bomb naval bases, but at night. With the fall of France, and the establishment of German naval bases on the French coast (notably Brest, Lorient, and Saint Nazaire, which contained major U-boat bases, and Brest was home to German heavy surface ships), the British bombed those bases, too. When the US entered the war, they also bombed these bases in France. Hundreds of raids flew against these targets, and Lorient and Saint Nazaire were largely destroyed (with relatively few civilian casualties, since the cities were largely evacuated before destruction), and La Pallice (by La Rochelle), Brest and Bordeaux were damaged. The U-boat pens were largely unharmed, as they were heavily protected by thick ferroconcrete armour, designed to be bomb-proof. German surface ships didn't fare so well: Scharnhorst was hit by five bombs in a raid on La Pallice on 24th July 1941; she was the star attraction that had brought the raid. Gneisenau, in Brest, was attacked many times, and was hit by a torpedo (dropped by a land-based torpedo bomber) on 6th April 1941, and by four bombs on 9th April. These continuing attacks motivated the dangerous "Channel Dash" (Operation Cerberus) of February 1942, to get these ships to safer bases in Germany.

These naval bases were poor targets for carrier attacks. The U-boat pens were immune to anything that carrier aircraft could drop on them, and raids would be small, against heavy AAA and fighter defences, and expose the carriers to dangerous German land-based air. British carriers did attack less-protected German naval bases, especially in Norway. German battleships were high-priority targets, and Tirpitz had been attacked 6 times by Bomber Command while in Wilhelmshaven and Kiel (to no effect), and attacks continued after she moved to bases in Norway. Tirpitz was attacked by Bomber Command 7 times while in Norwegian ports, the 3rd last attack causing major damage, and the last attack sinking her. There was also one attack by the Soviet air force, and two by midget submarines and manned torpedoes, and 5 attacks launched by carriers (two of which caused minor damage). Some other carrier strikes were attempted, but were cancelled due to bad weather. Other Norwegian ports were attacked, seeking lesser prey. British carriers ranged as far as the Arctic coast of Finland, on 30th July 1941, when Kirkenes (in northern Norway) and Petsamo (in Finland) were attacked, sinking one ship and damaging another (there were few targets in the ports).

British carriers earned their fame for attacks on naval bases against Italy, in the raid on Taranto, 11th November 1940. Three of the 6 Italian battleships were put out of action for some time. Ports in North Africa were attacked, too. Benghazi and Tripoli were raided, and carrier aircraft dropped flares and spotted for a battleship bombardment of Tripoli. British carriers would raid Japanese naval bases later in the war, too.

A German naval base was the target of the earliest known naval air raid, when a Japanese seaplane, based on the seaplane carrier Wakamiya, attacked the German naval base at Qingdao (Tsingtao), on 6th September 1914. The plane attacked the Austro-Hungarian cruiser Kaiserin Elisabeth, and a German gunboat. The bombs were dropped by hand, and missed. This attack, in the infancy of naval air power, was unsuccessful. Just over a quarter-century later, Taranto and Pearl Harbor would demonstrate what carrier power could do.

/u/Bigglesworth_ and /u/wotan_weevil have described the RAF's attacks on German ports. However, they have not fully explaned why the Royal Navy did not use its carriers to attack ports within Germany.

The Royal Navy had long appreciated the ability of aircraft to strike against German harbours. Officers of the Royal Naval Air Service had first suggested the use of aircraft to attack an enemy fleet in harbour in 1911. In 1912, a Lieutenant Hyde-Thomson wrote a paper describing the possibility of attacking targets with torpedo-carrying aircraft; he was soon sent to the Torpedo School in Portsmouth, to develop a torpedo that could be carried by an aircraft. This effort ultimately led to the development of the first carrier torpedo bomber, the Sopwith Cuckoo. Over the course of 1916-17, plans were developed for a strike against the German fleet using Cuckoos carried into position by a large fleet of carriers. This plan was overambitious, but the idea remained in place. Had the war continued into 1919, the German fleet would have been attacked by aircraft flying from the carriers Argus, Furious and Vindictive. While this attack never took place, the Fleet Air Arm continued to see attacks against enemy fleets in harbour as a key part of its mission. These strikes were often practiced in the interwar period, and plans were drawn up for them. The most famous of these was the plan for an attack on the Italian fleet base at Taranto, drawn up by the captain of Glorious in 1935 (and updated in 1938). However, despite this precedent, there was no attack on elements of the German fleet in German ports by FAA aircraft.

/u/Bigglesworth_ suggests that this was because the loss of Courageous in September 1939 led to the RN being more cautious with its carriers in the waters around the UK. However, I would disagree. Courageous was sunk in the Western Approaches, not the North Sea; in other words, on the wrong side of the UK. The RN was aware of the risks it took by deploying its carrier fleet on anti-submarine patrols, and was willing to take and suffer losses to it. British carriers continued to operate in the North Sea up until the fall of Norway. As an example, Ark Royal joined an operation by Home Fleet to support the damaged submarine Spearfish as it returned to the UK. This involved a deployment to the southern part of the North Sea. The loss of Courageous did, however, have a more indirect effect. Without her, the RN did not have enough carriers to carry out all the missions demanded of it, and to make an attack on German ports. The RN had to hunt German raiders, defend British interests in the Mediterranean and Far East, cover the Home Fleet against air attack and provide ships for training new pilots. After the loss of Courageous, the RN had six carriers available. Furious was undergoing a major refit and was unavailable. Argus was in the Mediterranean, training new pilots in deck-landings. Glorious was hunting raiders in the Indian Ocean. Hermes and Eagle were also hunting raiders, this time in the Atlantic; Ark Royal spent some time on this duty, some time with Home Fleet and some time in the Mediterranean. There was no carrier free to make an effective strike on German ports.

Another factor was the FAA's aircraft procurement policy. In the interwar period, British doctrine held that carrier aircraft would not be used against land-based aircraft. Carriers would fight other carriers or attack unprotected battleships at sea. This meant that carrier aircraft did not have to have comparable performance to those based on land. They could instead focus on the low-speed handling and strength that was useful for repeated landings on carriers. Fighters could carry two-man crews and have limited speed; the former allowed easier navigation, the latter was because the fighters would only have to fight low-performance carrier aircraft. The war showed this doctrine to be fatally flawed; there was no way for a carrier to avoid fighting land-based aircraft. To attack a German port, the strike aircraft might be attacked by high-performance fighters, while the fleet would be exposed to attack by bombers that could outrun its fighters. This was a high risk that the RN was unwilling to take; a strike against a German port could well end with heavy losses to the strike force and to the fleet that launched it. This risk could be avoided by making a surprise attack, as with the Taranto strike. However, this was harder to do in the North Sea than in the Mediterranean. There was much less sea room for a fleet to make deceptive manouvres. British bases were closer to Germany, and therefore much easier for the Germans to surveil. There were more German reconnaissance aircraft and submarines that might spot a fleet trying to approach the German coast. It was much simpler to allow the RAF to use its high-performance land-based aircraft to attack German ports. These could attack at less risk due to their higher performance and the difficulty the Germans had with attacking British air bases. RAF Bomber Command could, for much of the war, make attacks with much more aircraft than the RN could, increasing the chance of a successful attack.

Finally, there was a lack of targets that could be effectively attacked for much of the war. The German capital ships, the most valuable targets and those that were easiest to attack, spent a lot of time under repair, in the Baltic (which the FAA could not effectively reach) or out at sea. Ships out at sea could obviously not be attacked in harbour, while ships in drydock for repairs could not be targeted by torpedoes, the RN's main anti-ship weapon. The German large cruisers Scharnhorst and Gneisenau made their first sortie in November 1939, but suffered significant damage from wind and wave. Following this, they required repair and refit, which was followed by a trip to the Baltic for training. In April, they participated in the German invasion of Norway. Here, they took damage from British shells, mines and torpedoes, as well as some damage from the weather. Repairs put the ships out of action until the start of 1941, when they sortied for Operation Berlin, a raid into the North Atlantic. Operation Berlin ended in March 1941, when the two ships put into the French port of Brest. Here, they would be the target of frequent strikes from the RAF. Damage done by these strikes put them in and out of drydocks until they returned to Germany in the Channel Dash. Both ships struck mines during the voyage; Gneisenau would be destroyed by RAF bombers while repairing from this mine strike. After a prolonged series of repairs, Scharnhorst headed north to Norway, where she would be sunk off the North Cape by the British battleship Duke of York. Bismarck completed in August 1940, and spent the next eight months on sea trials in the Baltic. In May 1941, she would sortie from the Baltic into the Atlantic, and did not return. Her sister, Tirpitz, carried out sea trials in the Baltic, before heading to Norway. Here, she would be the target of a number of Fleet Air Arm strikes during 1944. This was at a time when the RN, through new construction and lend-lease, had sufficient carriers to carry out all the tasks required of it. It had new, modern aircraft (again largely acquired through lend-lease), and was attacking a less well-protected target than the German mainland.

Brilliant answers guys. Very in depth and make sense. Thank you